No plotInteractions.png after running optimizeSLIDE

[michanthchristopher]

Thank you for the tool. I'm not getting the plotInteractions.png when I run optimizeSLIDE. I thought setting do_interacts to TRUE would give this plot. Am I missing something? Is there another tool used to generate this?
Here's my yaml:

`---
x_path: /home/Projects/Scharer_sc/LRA.MAPseq/LRA_all/analysis/RNA.FB.VDJ/SLIDE/sledai.bcell.subsets.rp.mt.removed/sledai.slide.x.input.after.filtering.csv
y_path: /home/Projects/Scharer_sc/LRA.MAPseq/LRA_all/analysis/RNA.FB.VDJ/SLIDE/sledai.bcell.subsets.rp.mt.removed/sledai.slide.y.input.after.filtering.csv
out_path: /home/Projects/Scharer_sc/LRA.MAPseq/LRA_all/analysis/RNA.FB.VDJ/SLIDE/sledai.bcell.subsets.rp.mt.removed/out
delta:

• 0.01
• 0.1
  lambda:
• 0.5
• 1.0
  spec: 0.3
  y_factor: FALSE
  thresh_fdr: 0.2
  y_levels: NULL
  eval_type: corr
  SLIDE_iter: 1000
  SLIDE_top_feats: 10
  sampleCV_iter: 500
  sampleCV_K: 4
  do_interacts: TRUE`

[TranscriptionFactory]

Greetings!
Have you already tried running plotCorrelationNetworks (see step 2 at the bottom, here: https://github.com/jishnu-lab/SLIDE/blob/main/examples/testing.R)? optimize_SLIDE currently does not call the plotting functions, just runs SLIDE for different parameter combinations.

[michanthchristopher]

I have run plotCorrelationNetworks after opitimize_SLIDE, but not after performing cross validation like the link you sent suggested. Running cross validation now, then will retry plotCorrelationNetworks. Thank you!

[michanthchristopher]

I finished cross validation and ran plotCorrelationNetworks. This did not create the plotInteractions.png file. All that it creates are the interaction networks within each latent factor. I want to see how the latent factors are interacting.

[TranscriptionFactory]

Yes - my mistake. You are correct, the interaction plot should have run from SLIDE. Check the SLIDE_LFs.rds (see attached image) for values in the interaction_vars slot (to narrow down whether this a plotting issue or something else).

If this slot is blank, your spec value might be too high - have you tried using spec=0.1?

[michanthchristopher]

interaction_vars is populated

[TranscriptionFactory]

Greetings,
Apologies for the late response! It looks like there was a typo - thank you for catching this! Please update the SLIDE package and try this with your results:

SLIDE_LFs = readRDS('path/to/SLIDE_LFs.rds')
SLIDE::plotSigGenes(SLIDE_LFs, plot_interactions=T, out_path='path/you/want/to/save/results')